Material for the course Statistical Practice in Epidemiology with R
The 2026 edition runs 1–5 June 2026 in Tartu, Estonia.
| Directory | What is in it |
|---|---|
pracs-book/ |
The practicals, as R Markdown sources rendered to a bookdown book (HTML, PDF, EPUB), in two variants: exercise and with-solutions. Faculty edit only the *-e.rmd files. |
lectures/ |
One sub-folder per lecture. Source files + the compiled .pdf that ships to students. Each lecturer maintains their own folder. |
adm/ |
Course timetable (prog.tex, SPE-R-timetable.md) and historical post-mortems. |
misc/ |
Participant and faculty onboarding/reference docs (see below) plus a couple of helper R scripts. |
misc/SPE_participant_setup.md is the setup guide for course participants. It covers, step by step: installing R and an editor (RStudio or Positron), creating the course project, downloading the practical data, installing the required R packages (renv by default, plain install.packages() as a fallback), checking the setup, and where to find the timetable, lectures and practicals book (with and without solutions).
misc/SPE_faculty_setup.md is the single onboarding guide. It covers: installing git / R / RStudio / RTools, configuring RStudio to use git and bash, authenticating to GitHub (SSH or PAT), cloning the repo and restoring the renv environment, the daily pull → edit → commit → push loop, what to edit (and what NOT to edit), how to mark content as exercise-only or solution-only from a single source file, and how to build and preview the book locally.
Two GitHub Actions workflows publish the material automatically:
renderbook— renders the practicalsbookdownin HTML + PDF + EPUB, both the exercise and the with-solutions versions, and pushes them to thegh-pagesbranch. Visible at https://spe-r.github.io/SPE/SPE-R-2026-practicals/.Compile and build SPE-R GitHub material— compiles the lecture handouts, extracts the R solution scripts, builds the data and material zips, and pushes them to thegh-spe-materialbranch.
The companion repo SPE-R.github.io (the course landing page at https://spe-r.github.io/) links to the artifacts produced by both workflows.